After decades of decline, the Delta's vital signs have suddenly plunged to new depths. And its caretakers are baffled.

As part of the largest estuary on the West Coast, the Delta is a critical link in a chain of life that connects the Sierra Nevada to the Pacific Ocean. It is the single most important source of water in an arid state so big its economy ranks sixth among nations.

But CalFed, the program set up in 2000 to handle the competing demands for its water, and the Delta itself are in peril, according to a broad range of officials and outside critics.

By the end of this fiscal year, more than $3 billion will have been spent during the past five years on a program that was expected to bring across-the-board improvements.

Instead, each of the four pillars of the plan is falling short. Drinking water quality has worsened by some key measures. The aging levees that literally hold the Delta together remain largely neglected even as they have grown more vulnerable.

And although more water is being delivered out of the Delta, long-standing plans to increase Delta pumping remain on hold while water agencies express frustration over the lack of new reservoirs.

Most urgently, the Delta ecosystem is on the brink of collapse. Delta smelt, the key indicator of the Delta's overall health, is sliding toward extinction with alarming rapidity.

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"I believe that CalFed has failed, and died, but that no one directly involved is willing to admit it," said Peter Gleick, president of the Oakland-based environmental group Pacific Institute, in a letter to a state watchdog commission examining how the CalFed program is run.

In the Sept. 6 letter, Gleick agreed that the idea behind CalFed -- to foster cooperative ways to balance the state's need for water and a healthy environment -- is obviously a good one.

But, he noted, "The best approach from here may be to harvest the functioning organs that can still be used in another patient."

Consider:

The amount of water dedicated to restoring fish populations and the Delta environment has eroded through court decisions, regulatory changes and funding shortfalls. Environmentalists suspect the loss of water for environmental purposes has contributed to the fish crisis.

Water is saltier now during the critical fall months than before CalFed's earliest water management changes were put in place 10 years ago.

CalFed failed to even start a study of the vulnerability of the Delta's levees until earlier this year, missing a 2001 deadline. This comes on the heels of a 2004 levee failure and increasingly dire warnings from leading scientists about the fragility of the levees.

A core underpinning of CalFed was that water users would pay for programs that benefit them. But after five years, the program finally obtained a commitment for voluntary contributions only this month. Critics say it is inadequate..

In October, a state appeals court undercut the very foundation of CalFed, saying the environmental impact report that laid out the program failed to consider whether Southern California could get by with less Delta water, among other shortcomings.

It wasn't supposed to be this way.

Aug. 28, 2000, was a warm, sunny day in Sacramento when Gov. Gray Davis, standing on the steps of the Capitol, announced at an upbeat, decorous ceremony an agreement more than five years in the making.

The agreement included traditional adversaries; environmentalists, farmers, Southern California cities and Northern California interests all signed off on the plan. It included the state and federal government and a large number of government agencies.

By pledging cooperation and billions of dollars, there would be more water, it would be cleaner and the environment would improve markedly.

The agreement, known to bureaucrats and water wonks as the CalFed Record of Decision, was said to be the most ambitious ecosystem restoration program ever undertaken, anywhere. It was, simultaneously, the most extensive water management program in the world.

The plan would take 30 years. The first phase, to be completed by 2007, would cost $8.5 billion.

In a recent report by the Department of Finance, auditors cited progress in some areas while expressing frustration over the lack of measures it could use to gauge progress.

And yet there is broad agreement among those who signed on to the program that the idea behind CalFed was a good one, and that some version of the faltering program ought to continue.

CalFed's defenders point to the two most obvious successes of CalFed: improvements to salmon spawning habitat that have led to significantly higher salmon populations and a more cooperative approach to dealing with inevitable conflicts among farmers, cities and environmentalists over Delta water.

The program also has helped boost groundwater storage by 300,000 acre-feet, enough to fill Los Vaqueros Reservoir near Brentwood three times.

And, CalFed's supporters note, addressing California's intractable water conflicts was never going to be easy.

"The Bay-Delta is not subject to a quick fix," said Lester Snow, director of the state Department of Water Resources and one of the plan's early architects. "To blame CalFed for every slow-moving thing in California water, when all California water ever does is move slowly, is a real stretch."

Former Secretary of State Bill Jones, who sits on CalFed's governing board and was involved in early negotiations, said CalFed has not done as badly as it might appear. He said the program deserves a B- or C+.

"The problem is that the areas that failed really failed," he said.

With the deal cut in 2000 in hand, it would be foolish to scrap the program and further postpone tough decisions and deadlines that were set out that year.

For Jones, a supporter of San Joaquin Valley agriculture, those tough decisions mean building a new reservoir in Northern California and a canal to deliver water around the Delta.

"Don't let those deadlines slip," he said. "They're more important than ever, given the tragedy in New Orleans, the decline of Delta smelt ... and the need to move more water south."

Despite its importance to California's wildlife and economic well-being, the Delta remains largely out of sight and out of mind to the vast majority of Californians who care deeply about coastlines, redwood forests and the Sierra Nevada but remain largely ignorant about where their water comes from.

The Delta briefly got more attention in the early 1990s, when the state's thirst for the Delta's water, along with drought, combined to bring about an environmental crisis: Delta fish were being added to the list of protected species under the Endangered Species Act, and that in turn was forcing operators of the state's plumbing to cut back water supplies.

City water agencies, possessed with some reserves, were deeply concerned. Farmers, who needed the water for irrigation, were irate.

CalFed was borne out of that crisis, and the program's record of decision agreement was signed years later.

But now, after five years and nearly $3 billion spent since the agreement was signed, the Delta is again facing a similar crisis.

What went wrong?

Though firm answers to the biological collapse will have to wait, some of the reasons for policy failures have begun to emerge.

Following strong leadership on water issues by former governors Pete Wilson and Gray Davis, many contend Gov. Arnold Schwarzenegger came into office less committed to CalFed, although there are signs that is changing.

The Clinton administration was very involved in CalFed, but the Bush administration has been less so. The California congressional delegation has not always been unified on CalFed.

Patrick Wright, who led the effort until his resignation this year, was credited for pulling the plan together but criticized for lacking the political and management skills to see it through.

Others say the legislature, when it created the California Bay-Delta Authority to oversee CalFed, failed to give the new agency any real authority to make sure the program succeeded.

But the biggest failure, many observers and participants say, was the institutional unwillingness to confront the big conflicts in California water.

And who should pay to fix levees? The farmers protected by them? Taxpayers? Water utilities?

Are the levees even viable? Should the state build a peripheral canal around the Delta? Should it build new reservoirs? Who should pay for them?

When the record of decision was issued in 2000, state and federal government surpluses were high and CalFed's architects assumed conflicts could be eased if more was invested to improve habitat and water infrastructure.

But the surpluses dissipated and the money that was left may not have been spent effectively. CalFed never really adjusted to a new fiscal reality.

Now, that money is beginning to run out with about $750 million in bond funds left, enough for only two or three more years of a scaled-down plan unless new revenues are found.

"We gambled that we had a lot of time to figure it all out," said Gary Bobker, a program director at the Bay Institute, an environmental research group, and a member of the Bay-Delta Authority's public advisory board.

The realization that funds are running out and fish populations are crashing caught many off guard.